The CTU, based in Multinational base Tarin Kowt, has been led by the US since the Dutch left the province in 2010.

Col Stuart says the day-to-day running of the CTU won't change.

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Taking charge ... the Australian Army is now heading the withdrawal of troops from Afghanistan’s southern Oruzgan province.

“It's part of Australia taking its share of the load in the coalition. It sends a message that Australia is serious about making our contribution here in Afghanistan.

“It's a real privilege to command,” he says.

The leadership handover was enshrined with the exchanging of military colours in front of dignitaries including US General John Allen, the commander of all international forces in Afghanistan.

The Australian ambassador to Afghanistan, Paul Foley, the Australian chief of joint operations, Lieutenant Ash Power, and the local provincial governor and police chief were in attendance.

“Leadership of the Combined Team Oruzgan will help ensure that the transition... over the coming 12- to 15-month period is effected in a seamless way" ... Australian Defence Minister Stephen Smith.Credit:AP

In his acceptance speech, Col Stuart said he spent a moment in the morning by the base's memorial reading the names of the fallen to help him focus on his mission.

“Behind each name is a life cut short, and a family without a loved one today.”

Col Stuart also confirmed what the Defence Minister Stephen Smith said earlier this month, that the four Afghan National Army infantry battalions – known as Kandaks - that Australian troops are mentoring and training, will be declared operationally independent over the coming month.

“We're really now in a position where Afghan's can make decisions about their own future,” Col Stuart says.

There will be no increase in the troops Australia has stationed in Oruzgan, or other parts of Afghanistan.

The Combined Team Oruzgan was formed in 2010 after The Netherlands withdrew their troops from the NATO mission. It has since been under American control.

Mountainous Oruzgan, where Australia has about 1550 troops stationed, remains one of Afghanistan’s poorest and least developed provinces.

The population is overwhelmingly rural and most households rely on small subsistence farming. The literacy rate is five per cent, while eight per cent of homes have electricity.

A recent report from Tufts University, Winning the Hearts and Minds of Oruzgan Province, found that a decade of foreign troop presence had not brought peace.

It said: “Insecurity is largely the result of the failure of governance, which has exacerbated traditional rivalries. While historical rivalries may be a root cause, they have been hardened by corruption and poor governance along with the unintended consequence of international military force policies and actions.”

There has also been controversy around those Afghan nationals appointed to senior posts in the new Oruzgan administration.

Matiullah Khan, now police chief, was a warlord with his own private militia, who made millions providing "security" for coalition supply convoys.

The Dutch, who formerly led the NATO mission in Oruzgan, refused to work with him, citing his violent past and allegations of massive corruption.

Australian Prime Minister Julia Gillard visited Australia’s troops in the province last week, and told them their role would change over the next year.

“The assessment here in Oruzgan province is that what we are doing here is also on track,” she said.

“Now that means that there is still hard work to do but here for our troops, we will increasingly see, as we move through transition, our troops no longer engaging in partnered operations but moving to an advising and assisting role.”

Ms Gillard met Afghan President Hamid Karzai, raising concerns over the so-called "green-on-blue" attacks, in which Afghan troops turned their weapons on their NATO allies. Seven Australians have been killed by Afghan comrades.

“Clearly these have been tragic and disturbing incidents. They are designed to corrode morale and everything needs to be done on the Afghan side to deal with the possibility of insider attacks,” she said.

But the Prime Minister said, after 11 years of war in Afghanistan, the government was committed to “seeing the mission through”.